VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors.
\nThe following versions are installed on the CSF:<\/p>\n
VOTCA has not been tested using any of the existing gromacs installs.<\/p>\n
All users may use the software. All users should cite their use of the software as per the VOTCA Citations<\/a> webpage.<\/p>\n To access the executables please load one<\/em> of the appropriate modulefile:<\/p>\n Please do not run VOTCA on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n VOTCA is not suitable for serial jobs. Some components default to using all the cores available on a compute node and can therefore cause issues to other running jobs.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors. The following versions are installed on the CSF: Votca 1.2.3 – includes gromacs 4.6.0 (multi-threaded single precision only) in the VOTCA directory. VOTCA has not been tested using any of the existing gromacs installs. Restrictions on use All users may use.. Read more »<\/a><\/p>\n","protected":false},"author":11,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1129","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1129","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=1129"}],"version-history":[{"count":16,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1129\/revisions"}],"predecessor-version":[{"id":4976,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1129\/revisions\/4976"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=1129"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Set up procedure<\/h2>\n
module load apps\/intel-12.0\/votca\/1.2.3<\/pre>\n
Running the application<\/h2>\n
Serial batch job submission<\/h2>\n
Parallel batch job submission<\/h2>\n
\n
Westmere Intel nodes<\/h3>\n
#! \/bin\/bash -e\r\n#$ -cwd\r\n#$ -V\r\n#$ -l westmere\r\n#$ -pe smp.pe 12\r\n\r\ngrompp -v \r\n\r\nmdrun -v -nt $NSLOTS\r\n\r\necho Calculating distributions\r\ncsg_stat --top topol.tpr --trj traj.trr --cg hexane.xml --nt $NSLOTS --options fmatch.xml\r\n\r\necho \"Mapping confout.gro to get configuration for coarse-grained run\"\r\ncsg_map --top topol.tpr --trj confout.gro --cg hexane.xml --out conf_cg.gro<\/pre>\n
Further info<\/h2>\n
\n
man csg_stat<\/code><\/li>\n$VOTCA_HOME\/csg-tutorials<\/code><\/li>\n<\/ul>\nUpdates<\/h2>\n